estimating abundance of bins

[ne...@ualberta.ca]

Hi,

Could you recommend a way to calculate the relative abundance of each bin?

Thanks,

Camilla

[edgraham]

Hi Camilla,

There are a few ways to approach getting the relative abundance of each bin. One is to get the reads per base pair per genome and divide by the sum of all reads per base pairs per genomes and normalized by total read recruitment in the metagenome. A formula for this is shown in our paper on the genomes produced in the meditteranean:  https://doi.org/10.7717/peerj.3558. This can be easily calculated from the readcounts files produced in Binsanity-profile which has read counts per contig in the last column. 

The other method would be to use marker genes and get relative abundance based on the number of reads mapping back to the markers and normalizing by genome length. This formula is shown in pre-print paper here: https://doi.org/10.1101/162503. This method requires identifying the reads mapped back to each marker gene using bedtools or a similar program.

I am not sure if anyone has written a distributable tool to calculate this, but its something I can add to my list of things to get to next!

Regards,

Elaina

[cami...@gmail.com]

Great! Thanks,
Camilla